Organism : Pseudomonas aeruginosa | Module List :
PA1961

probable transcriptional regulator (NCBI)

CircVis
Functional Annotations (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA1961
(Mouseover regulator name to see its description)

PA1961 is regulated by 38 influences and regulates 3 modules.
Regulators for PA1961 (38)
Regulator Module Operator
PA0056 401 tf
PA0528 401 tf
PA0701 401 tf
PA1347 401 tf
PA1544 401 tf
PA2737 401 tf
PA3045 401 tf
PA3420 401 tf
PA3433 401 tf
PA3594 401 tf
PA3596 401 tf
PA3714 401 tf
PA3771 401 tf
PA3830 401 tf
PA4341 401 tf
PA4902 401 tf
PA5344 401 tf
PA5562 401 tf
PA0253 323 tf
PA0701 323 tf
PA0864 323 tf
PA0893 323 tf
PA1136 323 tf
PA1184 323 tf
PA1261 323 tf
PA1961 323 tf
PA2047 323 tf
PA2050 323 tf
PA2766 323 tf
PA3045 323 tf
PA3133 323 tf
PA3433 323 tf
PA3714 323 tf
PA3921 323 tf
PA4080 323 tf
PA4169 323 tf
PA4269 323 tf
PA5032 323 tf

Warning: PA1961 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
3472 2.30e-09 Cc.cacaT.GgatAatcagtTTT.
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3473 8.60e-06 CCAAtCaACGaaTaGTCGGt
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3626 1.00e+01 AattgaA.GA
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3627 1.40e+04 tAat.aCA.aTTgt
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Motif Help

Transcription factor binding motifs help to elucidate regulatory mechanism. cMonkey integrates powerful de novo motif detection to identify conditionally co-regulated sets of genes. De novo predicted motifs for each module are listed in the module page as motif logo images along with associated prediction statistics (e-values). The main module page also shows the location of these motifs within the upstream sequences of the module member genes.

Motifs of interest can be broadcasted to RegPredict (currently only available for Desulfovibrio vulgaris Hildenborough) in order to compare conservation in similar species. This integrated motif prediction and comparative analysis provides an additional checkpoint for regulatory motif prediction confidence.

Motif e-value: cMonkey tries to identify two motifs per modules in the upstream sequences of the module member genes. Motif e-value is an indicative of the motif co-occurences between the members of the module.Smaller e-values are indicative of significant sequence motifs. Our experience showed that e-values smaller than 10 are generally indicative of significant motifs.

Functional Enrichment for PA1961

PA1961 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for PA1961

PA1961 has total of 42 gene neighbors in modules 323, 401
Gene neighbors (42)
Gene Common Name Description Module membership
PA0224 PA0224 hypothetical protein (NCBI) 401, 489
PA0242 PA0242 hypothetical protein (NCBI) 156, 401
PA0244 PA0244 shikimate 5-dehydrogenase (NCBI) 372, 401
PA0254 PA0254 hypothetical protein (NCBI) 295, 323
PA0740 PA0740 probable beta-lactamase (NCBI) 323, 407
PA0823 PA0823 hypothetical protein (NCBI) 173, 323
PA0824 PA0824 hypothetical protein (NCBI) 173, 323
PA0825 PA0825 hypothetical protein (NCBI) 173, 323
PA0864 PA0864 probable transcriptional regulator (NCBI) 30, 323
PA0881 PA0881 hypothetical protein (NCBI) 401, 526
PA0986 PA0986 hypothetical protein (NCBI) 26, 323
PA0987 PA0987 hypothetical protein (NCBI) 173, 323
PA0989 PA0989 hypothetical protein (NCBI) 266, 323
PA1136 PA1136 probable transcriptional regulator (NCBI) 323, 432
PA1211 PA1211 hypothetical protein (NCBI) 401, 472
PA1212 PA1212 probable major facilitator superfamily (MFS) transporter (NCBI) 401, 472
PA1219 PA1219 hypothetical protein (NCBI) 74, 401
PA1310 phnW 2-aminoethylphosphonate:pyruvate aminotransferase (NCBI) 401, 425
PA1428 PA1428 hypothetical protein (NCBI) 24, 323
PA1961 PA1961 probable transcriptional regulator (NCBI) 323, 401
PA1962 acpD acyl carrier protein phosphodiesterase (NCBI) 323, 408
PA2766 PA2766 probable transcriptional regulator (NCBI) 266, 323
PA2767 PA2767 probable enoyl-CoA hydratase/isomerase (NCBI) 266, 323
PA2768 PA2768 hypothetical protein (NCBI) 266, 323
PA2810 PA2810 probable two-component sensor (NCBI) 401, 434
PA2819 PA2819 hypothetical protein (NCBI) 401, 461
PA2940 PA2940 probable acyl-CoA thiolase (NCBI) 211, 401
PA3044 PA3044 probable two-component sensor (NCBI) 105, 323
PA3064 pelA hypothetical protein (NCBI) 235, 401
PA3140 PA3140 hypothetical protein (NCBI) 321, 401
PA3360 PA3360 probable secretion protein (NCBI) 12, 401
PA3709 PA3709 probable major facilitator superfamily (MFS) transporter (NCBI) 401, 425
PA3893 PA3893 hypothetical protein (NCBI) 401, 545
PA4080 PA4080 probable response regulator (NCBI) 173, 323
PA4177 PA4177 hypothetical protein (NCBI) 394, 401
PA4341 PA4341 probable transcriptional regulator (NCBI) 401, 486
PA4621 PA4621 probable oxidoreductase (NCBI) 401, 517
PA4652 PA4652 hypothetical protein (NCBI) 401, 473
PA4903 PA4903 probable major facilitator superfamily (MFS) transporter (NCBI) 394, 401
PA4904 vanA vanillate O-demethylase oxygenase subunit (NCBI) 177, 323
PA5144 PA5144 hypothetical protein (NCBI) 177, 401
PA5284 PA5284 hypothetical protein (NCBI) 323, 498
Gene Page Help

Network Tab

If the gene is associated with a module(s), its connection to given modules along with other members of that module are shown as network by using CytoscapeWeb. In this view, each green colored circular nodes represent module member genes, purple colored diamonds represent module motifs and red triangles represent regulators. Each node is connected to module (Bicluster) via edges. This representation provides quick overview of all genes, regulators and motifs for modules. It also allows one to see shared genes/motifs/regulators among diferent modules.

Network representation is interactive. You can zoom in/out and move nodes/edges around. Clicking on a node will open up a window to give more details. For genes, Locus tag, organism, genomic coordinates, NCBI gene ID, whether it is transcription factor or not and any associated functional information will be shown. For regulators, number of modules are shown in addition to gene details. For motifs, e-value, consensus sequence and sequence logo will be shown. For modules, expression profile plot, motif information, functional associations and motif locations for each member of the module will be shown.
You can pin information boxes by using button in the box title and open up additional ones on the same screen for comparative analysis.

Regulation Tab

Regulation tab for each gene includes regulatory influences such as environmental factors or transcription factors or their combinations identified by regulatory network inference algorithms.

If the gene is a member of a module, regulators influencing that module are also considered to regulate the gene. Regulators table list total number of regulatory influences, regulators, modules and type of the influence.

You can see description of the regulator inside the tooltip when you mouseover. In certain cases the regulatory influence is predicted to be the result of the combination of two influences. These are indicated as combiner in the column labeled "Operator".

For transcription factors, an additional table next to regulator table will be show. This table show modules that are influenced by the transcription factor.

Motifs Tab

Network inference algorithm uses de novo motif prediction for assigning genes to modules. If there are any motifs identified in the upstream region of a gene, the motif will be shown here. For each motif sequence logo, consensus and e-value will be shown.

Functions Tab

Identification of functional enrichment for the module members is important in associating predicted motifs and regulatory influences with pathways. As described above, the network inference pipeline includes a functional enrichment module by which hypergeometric p-values are used to identify over representation of functional ontology terms among module members.

Network Portal presents functional ontologies from KEGG, GO, TIGRFAM, and COG as separate tables that include function name, type, corrected and uncorrected hypergeometric p-values, and the number of genes assigned to this category out of total number of genes in the module.

Module Members Tab

Identity of gene members in a module may help to identify potential interactions between different functional modules. Therefore, neighbor genes that share the same module(s) with gene under consideration are shown here. For each memebr, gene name, description and modules that contain it are listed.

Help Tab

This help page. More general help can be accessed by clicking help menu in the main navigation bar.

Social Tab

Network Portal is designed to promote collaboration through social interactions. Therefore interested researchers can share information, questions and updates for a particular gene.

Users can use their Disqus, Facebook, Twitter or Google accounts to connect to this page (We recommend Google). Each module and gene page includes comments tab that lists history of the interactions for that gene. You can browse the history, make updates, raise questions and share these activities with social web.

In the next releases of the network portal, we are planning to create personal space for each user where you can share you space that contains all the analysis steps you did along with relevant information.

CircVis

Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
  • 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
  • 2. Source gene
  • 3. Target genes (other module members)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend
Comments for PA1961
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Gene Help

Overview

Gene landing pages present genomic, functional, and regulatory information for individual genes. A circular visualization displays connections between the selected gene and genes in the same modules, with as edges drawn between the respective coordinates of the whole genome.

The gene page also lists functional ontology assignments, module membership, and motifs associated with these modules. Genes in the network inherit regulatory influences from the modules to which they belong. Therefore, the regulatory information for each gene is a collection of all regulatory influences on these modules. These are listed as a table that includes influence name, type, and target module. If the gene is a transcription factor, its target modules are also displayed in a table that provides residual values and number of genes.

CircVis

Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
  • 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
  • 2. Source gene
  • 3. Target genes (other module members)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend